importCDS: Import a seurat or scatter/scran CellDataSet object and...

In cole-trapnell-lab/monocle-release: Clustering, differential expression, and trajectory analysis for single- cell RNA-Seq

Description

This function takes a monocle CellDataSet and converts it to another type of object used in another popular single cell analysis toolkit. It currently supports Scran and Seurat packages.

Usage

importCDS(otherCDS, import_all = FALSE)

Arguments

otherCDS	the object you would like to convert into a monocle cds
import_all	Whether or not to import all the slots in seurat or scatter. Default is FALSE (or only keep minimal dataset).

Value

a new monocle cell dataset object converted from other objects (Scatter or Seurat).

Examples

## Not run: 
lung <- load_lung()
seurat_lung <- exportCDS(lung)
seurat_lung_all <- exportCDS(lung, export_all = T)
scater_lung <- exportCDS(lung, export_to = 'Scater')
scater_lung_all <- exportCDS(lung, export_to = 'Scater', export_all = T)

importCDS(seurat_lung)
importCDS(seurat_lung, import_all = T)
importCDS(seurat_lung_all)
importCDS(seurat_lung_all, import_all = T)
importCDS(scater_lung)
importCDS(scater_lung, import_all = T)
importCDS(scater_lung_all)
importCDS(scater_lung_all, import_all = T)

## End(Not run)

cole-trapnell-lab/monocle-release documentation built on May 13, 2019, 8:50 p.m.